Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_03893
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1733
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.25
Found at i:435 original size:135 final size:135
Alignment explanation
Indices: 193--598 Score: 679
Period size: 135 Copynumber: 3.0 Consensus size: 135
183 ACGAAAAAAT
* * * * *
193 GCTTCTAGTAATGCAACCAATAGCGAGCTGAAAAAGGATGAACCTTTGGAATCATCCAGTAGTGA
1 GCTTCTAGTAATACGACTAATAGCGAGCTGAAAAAGGATAAACCTTTGGAATCATCTAGTAGTGA
* *
258 TAGTTCTCAGAATTCTTGTCAAACAAATGGGGATTCAAGAACTGTAAAGCAAAATTGGCA-ACCG
66 TAGTTCTCAGAATTCTTGTCAAGCAAATGGGGATTCAAGAACTGTAAAGCAAAAATGG-AGACCG
*
322 ATTTCA
130 GTTTCA
* *
328 GCTTCTAGTAATACGAGTAATAGCAAGCTGAAAAAGGATAAACCTTTGGAATCATCTAGTAGTGA
1 GCTTCTAGTAATACGACTAATAGCGAGCTGAAAAAGGATAAACCTTTGGAATCATCTAGTAGTGA
*
393 TAATTCTCAGAATTCTTGTCAAGCAAATGGGGATTCAAGAACTGTAAAGCAAAAATGGAGACCGG
66 TAGTTCTCAGAATTCTTGTCAAGCAAATGGGGATTCAAGAACTGTAAAGCAAAAATGGAGACCGG
458 TTTCA
131 TTTCA
463 GCTTCTAGTAATACGACTAATAGCGAGCTGAAAAAGGATAAACCTTTGGAATCATCTAGTAGTGA
1 GCTTCTAGTAATACGACTAATAGCGAGCTGAAAAAGGATAAACCTTTGGAATCATCTAGTAGTGA
* *
528 TAGTTGTCAGAATTATTGTCAAGCAAATGGGGATTCAAGAACTGTAAAGCAAAAATGGAGACCGG
66 TAGTTCTCAGAATTCTTGTCAAGCAAATGGGGATTCAAGAACTGTAAAGCAAAAATGGAGACCGG
593 TTTCA
131 TTTCA
598 G
1 G
599 GAGGCATTGT
Statistics
Matches: 254, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
134 1 0.00
135 253 1.00
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.26
Consensus pattern (135 bp):
GCTTCTAGTAATACGACTAATAGCGAGCTGAAAAAGGATAAACCTTTGGAATCATCTAGTAGTGA
TAGTTCTCAGAATTCTTGTCAAGCAAATGGGGATTCAAGAACTGTAAAGCAAAAATGGAGACCGG
TTTCA
Done.